So far I've been considering:
1. Generate a custom reference (containing entries for all transgenic cassettes [1,2,etc]) for STAR, but then all (interesting) reads would end up being multimappers. Then postprocess with custom code.

2. Generate a single custom reference with a single barcode. Allow up to x mismatches during alignment (to allow for the different barcodes) and then postprocess the passing reads with custom code.

I'd like to avoid custom-coding (and reinventing the wheel) as much as possible obviously.
Appreciate any ideas. Thanks in advance!